Difference between revisions of "Molecular Dynamics Simulations Hemochromatosis"
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Bernhoferm (talk | contribs) (→Diary of "trial and error"-hell...) |
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| + | == Mutations == |
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| − | == Diary of "trial and error"-hell... == |
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| + | We have chosen R224W and C282S for the molecular dynamics simulations. C282S in order to see the impact of the broken disulfide bridge as well as its similarity to C282Y, one of the most common hemochromatosis mutations. R224W was chosen to further analyse this ambiguous mutation and maybe to finally clarify if it is malign or benign. |
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| − | Tipps for other groups: |
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| − | * AGroS wants to run "scwrl" and not "Scwrl4" which is the name after the installation. |
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| − | ** Solution: ln -s Scwrl4 scwrl |
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| − | * Problems NVT!!! (Can not open file: *_nvt.tpr). |
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| − | ** Solution: reduce to 16 cores (instead of 32) |
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| − | *** Anybody tried 32 cores on the real runs?? |
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| − | **** Yes, tried and it worked in the real run. The ''--partition=inter'' queue still throws segfaults on the NVT run, though.. ;) |
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| + | Molecular Dynamics Simulation runs: |
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| − | Current "test" state: |
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| − | * Run min I: solvent & fixed protein(SD) ...finished |
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| − | * Run min II: solvent & fixed backbone(SD) ...finished |
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| − | * Run min III: solvent & fixed backbone(CG) ...finished |
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| − | * Run NVT ...finished |
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| − | * Run NPT ...finished |
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| − | * Production run ...terminated after the 2 hour limit (without errors) |
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| − | Starting mutation runs: |
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* Wildtype (status: finished...) |
* Wildtype (status: finished...) |
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* R224W (status: running...) |
* R224W (status: running...) |
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Revision as of 12:56, 2 July 2012
Hemochromatosis>>Task 8: Molecular dynamics simulations
Contents
Riddle of the task
Sorry, not this week. Too busy... Meanwhile you could go on a journey or quest: Journey Quest
Short task description
Detailed description: Molecular dynamics simulations
Protocol
A protocol with a description of the data acquisition and other scripts used for this task is available here.
Mutations
We have chosen R224W and C282S for the molecular dynamics simulations. C282S in order to see the impact of the broken disulfide bridge as well as its similarity to C282Y, one of the most common hemochromatosis mutations. R224W was chosen to further analyse this ambiguous mutation and maybe to finally clarify if it is malign or benign.
Molecular Dynamics Simulation runs:
- Wildtype (status: finished...)
- R224W (status: running...)
- C282S (status: running...)
AGroS pipeline and intermediate PDB files
The different steps performed by AGroS:
- Runs RepairPDB and findBreaks, additional scripts to adapt PDB files to MD reality.
- Runs STRWater, an additional script that saves information for Structural Water Molecules in PDB file.
- Runs SCWRL, a program employed to correctly assign side chain information to PDB structures.
- Runs minimization in vacuum.
- Creates water box, includes solvent (water with 0.1 [NaCl]) and neutralizes protein intrinsic charge.
- Creates restrain files for each chain individually.
- Runs solvent minimization with fixed Protein (backbone + sidechains).
- Runs minimization with fixed Backbone.
- Runs minimization with fixed Backbone (CG).
- Runs short production NVT MD.
- Runs short production NPT MD.
- Runs Production MD.
Intermediate PDB files:
- 1a6zC.pdb (clashing water removed)
- 1a6zC_br.pdb (just the protein to find breaks)
- 1a6zC_br_0.pdb (same as above, but one file per chain)
- 1a6zC.pdb2 (hydrogens removed)
- 1a6zC_repair.pdb (without DNA and renumbered residues)
- 1a6zC_repair_0.pdb (same as above, but one file per chain)
- 1a6zC_water.pdb (structural water, B-Factor cutoff 15)
- 1a6zC_dna.pdb (just the DNA)
- 1a6zC_sc.pdb (SCWRL output for 1a6zC_repair.pdb)
- 1a6zC_nh.pdb (protein, plus structural water, plus DNA)
- 1a6zC_solv_tmp.pdb (ions added)
- 1a6zC_solv.pdb (duplicate water removed)
- 1a6zC_solv.pdb2 (protein, plus DNA)
- 1a6zC_solv_0.pdb (input to generate restrictions per chain)
- 1a6zC_solv_min.pdb (minimized solvent with fixed protein)
- 1a6zC_solv_min.pdb2 (just the protein)
- 1a6zC_solv_min_0.pdb (input to generate restrictions per chain)
- 1a6zC_solv_min2.pdb (minimization with fixed backbone)
- 1a6zC_solv_min3.pdb (minimization with fixed backbone, with conjugate gradient)
